VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Apr 16 2014 - 11:04:15 CDT

Mergemols takes a list argument. Should be:
set combined [::TopoTools::mergemols [list $solute $solvent]]
-Josh Vermaas

On 04/16/2014 10:07 AM, Ashish .Chauniyal wrote:
> Dear all,
>
> I have to merge two .pdb files into one and make a lammps data file
> out of it. Please can someone find what am I doing wrong, my TCL
> console says invalid command name "x" this x keeps on changing and I
> cant pinpoint where the error is. Here is the code.
>
>
> #topotools is already included
>
> mol new MG.xyz
> set Cusel [atomselect top "name H"]
> $Cusel set name Cu
> $Cusel set mass 63.54
> set Zrsel [atomselect top "name He"]
> $Zrsel set name Zr
> $Zrsel set mass 91.224
>
> set all [atomselect top "all"]
> $all writepdb leftside.pdb
>
> $all moveby {80.0 0.0 0.0}
> $all writepdb rightside.pdb
>
> #merging the two files
> set solute [mol new leftside.pdb]
> set solvent [mol new rightside.pdb]
> set combined [::TopoTools::mergemols "$solute $solvent"]
>
> $combined writepdb combine.pdb
> topo writelammpsdata data.composite atomic
>